SPM12 r6225

Author: SPMcentral

@file_array/Contents.m

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+% File Array Object
+%
+%   file_array   - create a file_array
+%   horzcat      - horizontal concatenation
+%   vertcat      - vertical concatenation
+%   size         - size of array
+%   length       - length of longest dimension
+%   subsref      - subscripted reference
+%   end          - last index in an indexing expression
+%   resize       - resize (but only of simple file_array structures)
+%
+%   other operations are unlikely to work.
+%
+% Example usage.
+%
+% % Create a file array object by mapping test_le.img
+% % to a 256x256x100 array, of datatype float32, stored
+% % in a little-endian way starting at byte 0.
+% fa0 = file_array('test_le.img',[256 256 100], 'FLOAT32-LE',0)
+%
+% % Creating an object from test_be.img, but skipping
+% % the first plane of data.  Data stored as big-endian
+% fa1 = file_array('test_be.img',[256 256 99], 'FLOAT32-BE',4*256*256)
+%
+% % Reshape procedure
+% fa2 = reshape(fa1,[128 2 256 99])
+%
+% % Concatenation
+% fa3 = [[fa0 fa0]; [fa0 fa0]]
+% fa4 = cat(3,fa0,fa1)
+%
+% % Note that reshape will not work on the above
+% % concatenated objects
+%
+% % Accessing values from the objects
+% img    = fa1(:,:,40);
+% pixval = fa4(50,50,:);
+% small  = fa1(1:2:end,1:2:end,40);
+%
+% % Determining dimensions
+% size(fa4)
+% size(fa2)
+% length(fa0)
+% _________________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: Contents.m 2696 2009-02-05 20:29:48Z guillaume $
+
+

@file_array/cat.m

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+function o = cat(dr,varargin)
+% Concatenate file_array objects.  The result is a non-simple object
+% that can no longer be reshaped.
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: cat.m 4136 2010-12-09 22:22:28Z guillaume $
+
+
+if dr>32 || dr<0, error('Unknown command option.'); end;
+dr   = max(round(dr),1);
+d    = ones(nargin-1,16);
+tmp  = {};
+dpos = 0;
+for i=1:nargin-1,
+    vi = varargin{i};
+    if strcmp(class(vi),'file_array')
+        sz                = size(vi);
+        d(i,1:length(sz)) = sz;
+        svi               = struct(vi);
+        svi               = svi(:);
+        for j=1:length(svi(:)),
+            if length(svi(j).pos)<dr
+                svi(j).pos((length(svi(j).pos)+1):dr) = 1;
+            end
+            svi(j).pos(dr)= svi(j).pos(dr) + dpos;
+        end;
+        dpos              = dpos + d(i,dr);
+        tmp{i}            = svi;
+    else
+        error(['Conversion to file_array from ' class(vi) ' is not possible.']);
+    end;
+end;
+if any(diff(d(:,[1:(dr-1) (dr+1):end]),1,1))
+    error('All matrices on a row in the bracketed expression must have the same number of rows.');
+else
+    o = vertcat(tmp{:});
+    o = file_array(o);
+end;

@file_array/ctranspose.m

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+function varargout = ctranspose(varargin)
+% Transposing not allowed
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: ctranspose.m 1143 2008-02-07 19:33:33Z spm $
+
+error('file_array objects can not be transposed.');

@file_array/disp.m

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+function disp(obj)
+% Display a file_array object
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: disp.m 4136 2010-12-09 22:22:28Z guillaume $
+
+
+if numel(struct(obj))>1,
+    fprintf('       %s object: ', class(obj));
+    sz = size(obj);
+    if length(sz)>4,
+        fprintf('%d-D\n',length(sz));
+    else
+        for i=1:(length(sz)-1),
+            fprintf('%d-by-',sz(i));
+        end;
+        fprintf('%d\n',sz(end));
+    end;
+else
+    disp(mystruct(obj))
+end;
+return;
+%=======================================================================
+
+%=======================================================================
+function t = mystruct(obj)
+fn = fieldnames(obj);
+for i=1:length(fn)
+    t.(fn{i}) = subsref(obj,struct('type','.','subs',fn{i}));
+end;
+return;
+%=======================================================================

@file_array/display.m

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+function display(obj)
+% Display a file_array object
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: display.m 1143 2008-02-07 19:33:33Z spm $
+
+
+disp(' ');
+disp([inputname(1),' = '])
+disp(' ');
+disp(obj)
+disp(' ')

@file_array/double.m

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+function out = double(fa)
+% Convert to double precision
+% FORMAT double(fa)
+% fa - a file_array
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: double.m 1143 2008-02-07 19:33:33Z spm $
+
+out = double(numeric(fa));
+

@file_array/end.m

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+function en = end(a,k,n)
+% Overloaded end function for file_array objects.
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: end.m 1143 2008-02-07 19:33:33Z spm $
+
+dim = size(a);
+if k>length(dim)
+    en = 1;
+else
+    if n<length(dim),
+    dim = [dim(1:(n-1)) prod(dim(n:end))];
+    end;
+    en = dim(k);
+end;

@file_array/fieldnames.m

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+function t = fieldnames(obj)
+% Fieldnames of a file-array object
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: fieldnames.m 1143 2008-02-07 19:33:33Z spm $
+
+t = {...
+    'fname'
+    'dim'
+    'dtype'
+    'offset'
+    'scl_slope'
+    'scl_inter'
+};

@file_array/file_array.m

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+function a = file_array(varargin)
+% Function for creating file_array objects.
+% FORMAT a = file_array(fname,dim,dtype,offset,scl_slope,scl_inter,permission)
+% a          - file_array object
+% fname      - filename
+% dim        - dimensions (default = [0 0] )
+% dtype      - datatype   (default = 'uint8-le')
+% offset     - offset into file (default = 0)
+% scl_slope  - scalefactor (default = 1)
+% scl_inter  - DC offset, such that dat = raw*scale + inter (default = 0)
+% permission - Write permission, either 'rw' or 'ro' (default = 'rw')
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: file_array.m 4136 2010-12-09 22:22:28Z guillaume $
+
+
+if nargin==1
+    if isstruct(varargin{1}),
+        a = class(varargin{1},'file_array');
+        return;
+    elseif isa(varargin{1},'file_array'),
+        a = varargin{1};
+        return;
+    end;
+end;
+a = struct('fname','','dim',[0 0],'dtype',2,...
+           'be',0,'offset',0,'pos',[],'scl_slope',[],'scl_inter',[], 'permission','rw');
+%a = class(a,'file_array');
+
+if nargin>=1, a =     fname(a,varargin{1}); end;
+if nargin>=2, a =       dim(a,varargin{2}); end;
+if nargin>=3, a =     dtype(a,varargin{3}); end;
+if nargin>=4, a =    offset(a,varargin{4}); end;
+if nargin>=5, a = scl_slope(a,varargin{5}); end;
+if nargin>=6, a = scl_inter(a,varargin{6}); end;
+if nargin>=7, a = permission(a,varargin{7}); end;
+
+a.pos = ones(size(a.dim));
+a     = file_array(a);
+

@file_array/horzcat.m

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+function o = horzcat(varargin)
+% Horizontal concatenation of file_array objects
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: horzcat.m 1143 2008-02-07 19:33:33Z spm $
+
+o    = cat(2,varargin{:});
+return;
+

@file_array/initialise.m

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+function initialise(fa)
+% Initialise file on disk
+%
+% This creates a file on disk with the appropriate size by explicitly
+% writing data to prevent a sparse file.
+%__________________________________________________________________________
+% Copyright (C) 2013 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: initialise.m 5458 2013-05-01 14:32:23Z guillaume $
+
+
+% first approach
+% fa = subsasgn(fa, substruct('()',num2cell(size(fa))), 0);
+
+% second approach
+% fa = subsasgn(fa, substruct('()',repmat({':'},1,ndims(fa))), 0);
+
+% third approach (problem if n > intmax('int32'))
+% bs = 2^20;
+% n  = prod(size(fa)); %#ok<PSIZE>
+% fa = reshape(fa,n,1);
+% for i=1:ceil(n/bs)
+%    ii = ((((i-1)*bs)+1):min((i*bs),n))';
+%    fa = subsasgn(fa,struct('type','()','subs',{{ii}}),zeros(numel(ii),1));
+% end
+
+d  = datatypes;
+dt = find(cat(1,d.code)==fa.dtype);
+if isempty(dt), error('Unknown datatype.'); end
+d  = d(dt);
+nbytes = d.nelem * d.size * prod(size(fa)); %#ok<PSIZE>
+init(fa.fname, nbytes, struct('offset',fa.offset));

@file_array/isnan.m

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+function out = isnan(fa)
+% Convert to numeric form
+% FORMAT isnan(fa)
+% fa - a file_array
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: isnan.m 1301 2008-04-03 13:21:44Z john $
+
+bs  = 10240;
+m   = size(fa);
+fa  = reshape(fa,prod(m),1);
+n   = prod(m);
+out = false(m);
+for i=1:ceil(n/bs),
+    ii      = ((((i-1)*bs)+1):min((i*bs),n))';
+    tmp     = subsref(fa,struct('type','()','subs',{{ii}}));
+    out(ii) = isnan(tmp);
+end
+

@file_array/length.m

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+function l = length(x)
+% Overloaded length function for file_array objects
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: length.m 1143 2008-02-07 19:33:33Z spm $
+
+
+l = max(size(x));
+

@file_array/loadobj.m

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+function b = loadobj(a)
+% loadobj for file_array class
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: loadobj.m 1544 2008-05-06 10:34:36Z guillaume $
+
+if isa(a,'file_array')
+    b = a;
+else
+    a = permission(a, 'rw');
+    b = file_array(a);
+end

@file_array/ndims.m

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+function out = ndims(fa)
+% Number of dimensions
+%_______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: ndims.m 1143 2008-02-07 19:33:33Z spm $
+
+
+out = size(fa);
+out = length(out);
+

@file_array/numel.m

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+function t = numel(obj)
+% Number of simple file arrays involved.
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: numel.m 1143 2008-02-07 19:33:33Z spm $
+
+
+% Should be this, but it causes problems when accessing
+% obj as a structure.
+%t = prod(size(obj));
+
+t  = numel(struct(obj));

@file_array/numeric.m

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+function out = numeric(fa)
+% Convert to numeric form
+% FORMAT numeric(fa)
+% fa - a file_array
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: numeric.m 1143 2008-02-07 19:33:33Z spm $
+
+
+[vo{1:ndims(fa)}] = deal(':');
+out = subsref(fa,struct('type','()','subs',{vo}));
+

@file_array/permute.m

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+function varargout = permute(varargin)
+% Can not be permuted.
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: permute.m 1143 2008-02-07 19:33:33Z spm $
+
+
+error('file_array objects can not be permuted.');